All Jobs Error Out

All Jobs Error Out

Hi all,

This afternoon, our local instance of Galaxy suddenly started producing errors for all jobs. This is the trace that gets printed out. Not sure what is happening because the error doesn’t give much information other than python not being able to find a module.

Traceback (most recent call last):
File "/localdata1/galaxy/database/jobs_directory/002/2931/set_metadata_LMpe2m.py", line 1, in
from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()
File "/localdata1/galaxy/lib/galaxy_ext/metadata/set_metadata.py", line 25, in
import galaxy.model.mapping # need to load this before we unpickle, in order to setup properties assigned by the mappers
File "/localdata1/galaxy/lib/galaxy/model/mapping.py", line 19, in
from galaxy.model.custom_types import JSONType, MetadataType, TrimmedString, UUIDType
File "/localdata1/galaxy/lib/galaxy/model/custom_types.py", line 13, in
from galaxy import app
File "/localdata1/galaxy/lib/galaxy/app.py", line 17, in
from galaxy.visualization.plugins.registry import VisualizationsRegistry
File "/localdata1/galaxy/lib/galaxy/visualization/plugins/registry.py", line 15, in
from galaxy.visualization.plugins import plugin as vis_plugins
File "/localdata1/galaxy/lib/galaxy/visualization/plugins/plugin.py", line 13, in
from galaxy.web.base import interactive_environments
File "/localdata1/galaxy/lib/galaxy/web/base/interactive_environments.py", line 14, in
from galaxy.tools.deps.docker_util import DockerVolume
File "/localdata1/galaxy/lib/galaxy/tools/__init__.py", line 60, in
import tool_shed.util.repository_util as repository_util
File "/localdata1/galaxy/lib/tool_shed/util/repository_util.py", line 16, in
from tool_shed.util import hg_util
File "/localdata1/galaxy/lib/tool_shed/util/hg_util.py", line 11, in
from mercurial.exchange import readbundle
File "/lib64/python2.7/site-packages/mercurial/exchange.py", line 18, in
from . import (
File "/lib64/python2.7/site-packages/mercurial/bundle2.py", line 168, in
urlerr = util.urlerr
AttributeError: 'module' object has no attribute 'urlerr'

Could anyone provide any insight on the issue? Thanks!
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> Hi all,
>
> This afternoon, our local instance of Galaxy suddenly started producing errors for all jobs. This is the trace that gets printed out. Not sure what is happening because the error doesn’t give much information other than python not being able to find a module.
>
> Traceback (most recent call last):
> File "/localdata1/galaxy/database/jobs_directory/002/2931/set_metadata_LMpe2m.py", line 1, in
> from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()
> File "/localdata1/galaxy/lib/galaxy_ext/metadata/set_metadata.py", line 25, in
> import galaxy.model.mapping # need to load this before we unpickle, in order to setup properties assigned by the mappers
> File "/localdata1/galaxy/lib/galaxy/model/mapping.py", line 19, in
> from galaxy.model.custom_types import JSONType, MetadataType, TrimmedString, UUIDType
> File "/localdata1/galaxy/lib/galaxy/model/custom_types.py", line 13, in
> from galaxy import app
> File "/localdata1/galaxy/lib/galaxy/app.py", line 17, in
> from galaxy.visualization.plugins.registry import VisualizationsRegistry
> File "/localdata1/galaxy/lib/galaxy/visualization/plugins/registry.py", line 15, in
> from galaxy.visualization.plugins import plugin as vis_plugins
> File "/localdata1/galaxy/lib/galaxy/visualization/plugins/plugin.py", line 13, in
> from galaxy.web.base import interactive_environments
> File "/localdata1/galaxy/lib/galaxy/web/base/interactive_environments.py", line 14, in
> from galaxy.tools.deps.docker_util import DockerVolume
> File "/localdata1/galaxy/lib/galaxy/tools/__init__.py", line 60, in
> import tool_shed.util.repository_util as repository_util
> File "/localdata1/galaxy/lib/tool_shed/util/repository_util.py", line 16, in
> from tool_shed.util import hg_util
> File "/localdata1/galaxy/lib/tool_shed/util/hg_util.py", line 11, in
> from mercurial.exchange import readbundle
> File "/lib64/python2.7/site-packages/mercurial/exchange.py", line 18, in
> from . import (
> File "/lib64/python2.7/site-packages/mercurial/bundle2.py", line 168, in
> urlerr = util.urlerr
> AttributeError: 'module' object has no attribute 'urlerr'
>
> Could anyone provide any insight on the issue? Thanks!
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
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> and other Galaxy lists, please use the interface at:
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Re: All Jobs Error Out

Hi John,

Thanks for the reply. I saw in the stack trace that there was a issue with mercurial, which was recently installed in the system. After uninstalling it, everything ran again. Not entirely sure what happened.

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